ID   NIFA_HERSE              Reviewed;         542 AA.
AC   P27713;
DT   01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1992, sequence version 1.
DT   03-AUG-2022, entry version 113.
DE   RecName: Full=Nif-specific regulatory protein;
GN   Name=nifA;
OS   Herbaspirillum seropedicae.
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Oxalobacteraceae; Herbaspirillum.
OX   NCBI_TaxID=964;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=Z78 / ATCC 35893 / DSM 6446 / LMG 6514;
RX   PubMed=1840608; DOI=10.1099/00221287-137-7-1511;
RA   Souza E.M., Funayama S., Rigo L.U., Yates M.G., Pedrosa F.O.;
RT   "Sequence and structural organization of a nif A-like gene and part of a
RT   nifB-like gene of Herbaspirillum seropedicae strain Z78.";
RL   J. Gen. Microbiol. 137:1511-1522(1991).
CC   -!- FUNCTION: Required for activation of most nif operons, which are
CC       directly involved in nitrogen fixation.
CC   -!- SUBUNIT: Interacts with sigma-54.
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DR   EMBL; M60319; AAA25027.1; -; Genomic_DNA.
DR   PIR; A44813; A44813.
DR   AlphaFoldDB; P27713; -.
DR   SMR; P27713; -.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0043565; F:sequence-specific DNA binding; IEA:InterPro.
DR   GO; GO:0009399; P:nitrogen fixation; IEA:UniProtKB-KW.
DR   GO; GO:0000160; P:phosphorelay signal transduction system; IEA:UniProtKB-KW.
DR   GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:CACAO.
DR   Gene3D; 3.30.450.40; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   InterPro; IPR003593; AAA+_ATPase.
DR   InterPro; IPR003018; GAF.
DR   InterPro; IPR029016; GAF-like_dom_sf.
DR   InterPro; IPR009057; Homeobox-like_sf.
DR   InterPro; IPR002197; HTH_Fis.
DR   InterPro; IPR010113; Nif-specific_regulatory_prot.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR002078; Sigma_54_int.
DR   InterPro; IPR025662; Sigma_54_int_dom_ATP-bd_1.
DR   InterPro; IPR025943; Sigma_54_int_dom_ATP-bd_2.
DR   InterPro; IPR025944; Sigma_54_int_dom_CS.
DR   Pfam; PF01590; GAF; 1.
DR   Pfam; PF02954; HTH_8; 1.
DR   Pfam; PF00158; Sigma54_activat; 1.
DR   PRINTS; PR01590; HTHFIS.
DR   SMART; SM00382; AAA; 1.
DR   SMART; SM00065; GAF; 1.
DR   SUPFAM; SSF46689; SSF46689; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   TIGRFAMs; TIGR01817; nifA; 1.
DR   PROSITE; PS00675; SIGMA54_INTERACT_1; 1.
DR   PROSITE; PS00676; SIGMA54_INTERACT_2; 1.
DR   PROSITE; PS00688; SIGMA54_INTERACT_3; 1.
DR   PROSITE; PS50045; SIGMA54_INTERACT_4; 1.
PE   4: Predicted;
KW   Activator; ATP-binding; DNA-binding; Metal-binding; Nitrogen fixation;
KW   Nucleotide-binding; Transcription; Transcription regulation;
KW   Two-component regulatory system.
FT   CHAIN           1..542
FT                   /note="Nif-specific regulatory protein"
FT                   /id="PRO_0000081307"
FT   DOMAIN          29..170
FT                   /note="GAF"
FT   DOMAIN          203..432
FT                   /note="Sigma-54 factor interaction"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   DNA_BIND        514..533
FT                   /note="H-T-H motif"
FT                   /evidence="ECO:0000250"
FT   REGION          433..499
FT                   /note="Inter-domain linker"
FT   REGION          500..542
FT                   /note="C-terminal DNA-binding domain"
FT   BINDING         231..238
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   BINDING         294..303
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   BINDING         446
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250|UniProtKB:P05407"
FT   BINDING         451
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250|UniProtKB:P05407"
SQ   SEQUENCE   542 AA;  60880 MW;  3A0BD14B14390AA5 CRC64;
     MATILDDRSV NLELVTIYEI SKILGSSLDL SKTLREVLNV LSAHLETKRV LLSLMQDSGE
     LQLVSAIGLS YEEFQSGRYR VGEGITGKIF QTETPIVVRD LAQEPLFLAR TSPRQSQDGE
     VISFVGVPIK AAREMLGVLC VFRDGQSPSR SVDHEVRLLT MVANLIGQTV RLYRSVAAER
     QQLQEEKRQL SRQLQGKYKL DNVIGISKAM QEVFAQVHQS APSRSTMLLR GESGTGKEVI
     ARAIHYLSPR KDGPFIKVNC AALSETLLES ELFGHEKGAF TGAQGERKGR FELAHGGTLF
     LDEIGEISPA FQAKLLRVLQ EREFERVGGS RSIKVDVRLV TATNRDLEKA VAKGEFRADL
     YYRINVVSIF IPPLRERRED IPYLVEHFLE KFRVENQRAM VAMSPQAMKV MMNCYWPGNV
     RELENCVERT ATMMRGDLIT EVHFSCQQNK CLTKVLHEPG QQQPVVVVPL ERISAPYGAI
     FAEWDGQGQA TGAAPPTSER ERLIWAMEQC GWVQAKAARA LNISPRQMGY ALQKFNIEVK
     KF